The present study demonstrated application of appropriate modern molecular techniques that are suitable for rapid S. cerevisiae strain identification and further testing of various strains for their technological potential. The combination of used modern molecular techniques including species-specific primers, and interdelta PCR typing enabled us to identify S. cerevisiae at strain level. Also important physiological characteristics of the yeasts used in this study are suitable for rapid selection of the different S. cerevisiae strains that can be applied in the winemaking process. Application of the selected strains with suitable technological properties in the wine fermentation process should increase the quality of the wine and enhance the regional character of traditional Moravian wines. Hence, some isolated indigenous strains will be tested in a large-scale fermentation process by a small Moravian winery